Three critical ecosystems of the Skagit Basin have been identified as vulnerable to the impacts of climate change: terrestrial, freshwater and marine. The responses of the terrestrial ecosystems to climate change focus on forested lands. The Skagit hosts a healthy forest in the upper areas of the Basin. However, projections of drier, warmer summers could favor the proliferation of more drought-tolerant tree species, to the detriment of the species that rely on wetter conditions. Drought-intolerant species, like western red cedar and Sitka spruce, could suffer population losses. Overall, the habitats suitable for Douglas-Fir, an economically important forest species in the Skagit basin, are projected to decline across the state. Hot, dry summers tend to weaken pine tree species making them susceptible to mountain pine beetle outbreaks and to forest fires.
The Skagit Basin provides important habitat for endangered fish species such as Chinook salmon, steelhead and bull trout. The climate-induced hydrologic shifts in the Skagit Basin will alter the freshwater habitat that these and other fish species depend on for survival. The projections of increased flood severity in the winters, for example, could result in scouring of the salmon redds (overwinter nests for the eggs), and sweep juveniles downstream before they are mature enough to migrate. More intense low flows in the summer will exacerbate higher water temperatures and create migration barriers for spawning adult salmon. Finally, increased forest disturbance, from fire or higher mortality resulting from insect outbreaks, may impact water quality..
The major foreseeable impacts to marine habitats near the Skagit River outlets will be climate-induced changes in sea levels and sediment delivery to the coastal areas. These two factors are entrenched in a cycle that will result in tidal marsh loss and a conversion of marsh and beach habitats to saltmarsh or tidal flats. The transformation of nearshore habitats, in combination with a loss of eelgrass abundance, will be detrimental to economically important species, like Dungeness crabs and juvenile salmon that depend on the current conditions.